Antigen

Antigen Class

TFs and others

Antigen

RELA

Cell type

Cell type Class

Kidney

Cell type

Renal cell carcinoma

NA

NA

Sample

source_name

ccRCC cell line

transcription factor

NFkB

chip antibody

NFĸB p65 (sc-372, Santa Cruz)

source

786-O (ATCC CRL1932)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For each transcription factor, ~3x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 1.5 ml and the amount of antibody used was 15 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 6 times with wash buffer at room temperature. Amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB)

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

71012417

Reads aligned (%)

85.9

Duplicates removed (%)

38.5

Number of peaks

16656 (qval < 1E-05)

hg19

Number of total reads

71012417

Reads aligned (%)

85.5

Duplicates removed (%)

39.2

Number of peaks

16327 (qval < 1E-05)